Re: [Gusdev-gusdev] Re: LoadTaxon.pm

[Jonathan C. <cra...@pc...>]

Hi Arnaud-

I agree with Martin about the "EOF on communication channel" error; all
this message means is that something happened to break your connection
to the database.  What broke your connection was almost certainly the
server process crashing or shutting down in response to the *other* error
("hostdef extension doesn't exist").  I've never seen this error before
and have no idea what might have caused it.  You could try looking at the
trace file dumped by Oracle when the process crashed to see what it was
doing at the time.

As for the problem running the plugin when the --commit flag is not
specified, I'm surprised that it crashes; the foreign key dependencies
should be created just fine in no-commit mode.  However, all the inserts
do have to performed within a single transaction, which is then rolled
back before the plugin exits.  Maybe the LoadTaxon plugin is doing
something to cause a premature rollback?

Arnaud Kerhornou wrote:
> Another thing. At some point the code is trying to analyse the 
> SRes.TaxonName table. I've got an insufficient privileges error.

At the very least the plugin should have an option to let the user
specify whether they want to analyze the table, since not every site
will want to allow regular users the necessary privileges.

Jonathan

-- 
Jonathan Crabtree
Center for Bioinformatics, University of Pennsylvania
1406 Blockley Hall, 423 Guardian Drive Philadelphia, PA 19104-6021
215-573-3115